/tools/filters/grep.xml

 1<tool id="Grep1" name="Select">
 2  <description>lines that match an expression</description>
 3  <command interpreter="python">grep.py -i $input -o $out_file1 -pattern '$pattern' -v $invert</command>
 4  <inputs>
 5    <param format="txt" name="input" type="data" label="Select lines from"/>
 6    <param name="invert" type="select" label="that">
 7      <option value="false">Matching</option>
 8      <option value="true">NOT Matching</option>
 9    </param>
10    <param name="pattern" size="40" type="text" value="^chr([0-9A-Za-z])+" label="the pattern" help="here you can enter text or regular expression (for syntax check lower part of this frame)"/>
11  </inputs>
12  <outputs>
13    <data format="input" name="out_file1" metadata_source="input"/>
14  </outputs>
15  <tests>
16    <test>
17      <param name="input" value="1.bed"/>
18      <param name="invert" value="false"/>
19      <param name="pattern" value="^chr[0-9]*"/>
20      <output name="out_file1" file="fs-grep.dat"/>
21    </test>
22  </tests>
23  <help>
24
25.. class:: infomark
26
27**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
28
29-----
30
31**Syntax**
32
33The select tool searches the data for lines containing or not containing a match to the given pattern. Regular Expression is introduced in this tool. A Regular Expression is a pattern descibing a certain amount of text. 
34
35- **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
36- **\\A** matches the beginning of a string(but not an internal line).
37- **\\d** matches a digit, same as [0-9].
38- **\\D** matches a non-digit.
39- **\\s** matches a whitespace character.
40- **\\S** matches anything BUT a whitespace.
41- **\\t** matches a tab.
42- **\\w** matches an alphanumeric character.
43- **\\W** matches anything but an alphanumeric character.
44- **(** .. **)** groups a particular pattern.
45- **\\Z** matches the end of a string(but not a internal line).
46- **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
47
48  - **{n}** The preceding item is matched exactly n times.
49  - **{n,}** The preceding item ismatched n or more times. 
50  - **{n,m}** The preceding item is matched at least n times but not more than m times. 
51
52- **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
53- **.** Matches any single character except a newline.
54- ***** The preceding item will be matched zero or more times.
55- **?** The preceding item is optional and matched at most once.
56- **+** The preceding item will be matched one or more times.
57- **^** has two meaning:
58  - matches the beginning of a line or string. 
59  - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
60- **$** matches the end of a line or string.
61- **\|** Separates alternate possibilities. 
62
63-----
64
65**Example**
66
67- **^chr([0-9A-Za-z])+** would match lines that begin with chromsomes, such as lines in a BED format file.
68- **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
69- **([^,][0-9]{1,3})(,[0-9]{3})\*** would match a large integer that is properly seperated with commas such as 23,078,651.
70- **(abc)|(def)** would match either "abc" or "def".
71- **^\\W+#** would match any line that is a comment.
72</help>
73</tool>